Background and purpose: Short-term external counterpulsation (ECP) noninvasively augments cerebral blood flow by elevating blood pressure in ischemic stroke. The current retrospective case–control study examined the effect of long-term ECP treatment on blood pressure and beat-to-beat blood pressure variability (BPV) in patients with recent ischemic stroke. Method: The ECP group included data from 20 recent ischemic stroke patients who received five daily 1 h sessions each week for seven weeks, for a total of 35 sessions of ECP treatment from our ECP registry. An equivalent comparative control group without ECP treatment was composed from the same pool of patients and matched with cases by sex and age. Beat-to-beat heart rate and blood pressure were monitored before and after the long-term intervention. Power spectral analysis calculated the beat-to-beat BPV oscillations at very low frequency (VLF; <0.04 Hz), low frequency (LF; 0.04–0.15 Hz), high frequency (HF; 0.15–0.40 Hz), and the total power spectral density (TP; <0.40 Hz) and LF/HF ratio. Result: There was a significant reduction in systolic blood pressure (SBP) after the intervention compared with that before intervention in both groups (p < 0.05), but only the ECP group displayed a statistically significant reduction in diastolic blood pressure (DBP) (p = 0.023). The changes in SBP and DBP (delta SBP and delta DBP) from pre-intervention to completion showed no significant differences between the two groups (all p > 0.05). The ECP group exhibited a more pronounced and significant decrease in each spectral component of BPV after the intervention than at pre-intervention, with a substantial decrease in systolic BPV at TP (p = 0.048) and in the LF/HF ratios (p = 0.021 in diastolic BPV and p = 0.004 in systolic BPV, respectively) compared to the control group. Conclusions: A standard 35-session ECP treatment decreases beat-to-beat BPV but does not change SBP and DBP in patients with recent ischemic stroke. This implies that long-term ECP treatment may enhance autonomic regulation to benefit post-stroke clinical outcomes.